The pace at which the genetics of cancer is being deciphered has been accelerating. Researchers have begun to characterize in detail multiple genetic mechanisms that give rise to cancer, as well as numerous functional pathways associated with cancer, such as damage response, cell cycle, cell proliferation, and cell death. This exponential growth in our knowledge base of cancer genetics has led to the identification of a large array of genes, proteins and pathways that potentially play a central role in carcinogenesis and/or may be potential targets for therapeutic intervention. The challenge now is to experimentally delve deeper, both into how these genes function and interrelate in vivo and in vitro, and also into how different compounds and compound classes influence these genes. Althea Technologies proposes the development of a new, production-oriented, high-throughput, rtPCR-based approach to gene expression analysis. The proposed methods involve performing multiplexed rtPCR using a universal primer strategy, and further integrating the rtPCR step with the high-density capabilities of the microarray-format readout for analysis. The potential advantages of the method include (a) high throughput sample processing, (b) high detection sensitivity, opening the door to multiplexed gene expression analysis of very small amounts of tissue, and (c) a targeted cost per data point of 1 or a few pennies per gene. The Specific Aims for Phase I are focused on (1) demonstrating the proof of principle of the approach and (2) providing the roadmap for automating much of the process, a process that manages samples from cells and/or cell culture through to data acquisition and analysis.